The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000527.5(LDLR):c.2475C>G (p.Asn825Lys)

CA023675

161265 (ClinVar)

Gene: LDLR
Condition: hypercholesterolemia, familial
Inheritance Mode: Semidominant inheritance
UUID: a366bd5f-25ad-4977-b948-cb45aa320c0c

HGVS expressions

NM_000527.5:c.2475C>G
NM_000527.5(LDLR):c.2475C>G (p.Asn825Lys)
NC_000019.10:g.11129598C>G
CM000681.2:g.11129598C>G
NC_000019.9:g.11240274C>G
CM000681.1:g.11240274C>G
NC_000019.8:g.11101274C>G
NG_009060.1:g.45218C>G
ENST00000558518.6:c.2475C>G
ENST00000252444.9:n.2729C>G
ENST00000455727.6:c.1971C>G
ENST00000535915.5:c.2352C>G
ENST00000545707.5:c.1941C>G
ENST00000557933.5:c.2537C>G
ENST00000558013.5:c.2475C>G
ENST00000558518.5:c.2475C>G
ENST00000560628.1:n.108+1944C>G
NM_000527.4:c.2475C>G
NM_001195798.1:c.2475C>G
NM_001195799.1:c.2352C>G
NM_001195800.1:c.1971C>G
NM_001195803.1:c.1941C>G
NM_001195798.2:c.2475C>G
NM_001195799.2:c.2352C>G
NM_001195800.2:c.1971C>G
NM_001195803.2:c.1941C>G

Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 5
PS1 PP4 PP3 PM2 PS4_Supporting
Not Met criteria codes 1
PS3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Familial Hypercholesterolemia Expert Panel Specifications to the ACMG/AMP Variant Classification Guidelines Version 1.2

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Familial Hypercholesterolemia VCEP
The NM_000527.5 (LDLR):c.2475C>G (p.Asn825Lys) variant is classified as Likely Pathogenic for Familial Hypercholesterolemia by applying evidence codes (PM2, PP3, PS1, PP4, PS4_Supporting) as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012). The supporting evidence is as follows: PM2: PopMax MAF = 0.00002 in European (Non-Finnish) in gnomAD (gnomAD v2.1.1). PP3: REVEL = 0.803. PS1: One other missense variant that leads to the same amino acid change at same codon, NM_000527.5 (LDLR):c.2475C>A (p.Asn825Lys), (ClinVarID 252341), is classified as Pathogenic by these guidelines. PP4: Variant meets PM2 and is identified in >1 index cases who fulfil FH diagnostic criteria after alternative causes of high cholesterol were excluded. PS4_Supporting: Variant meets PM2 and is identified in 5 index cases who fulfil FH diagnostic criteria. Four index cases met DLCN criteria for definite or probable FH: 1 case from Department of Medicine and Cardiology, Aarhus Amtssygehus University Hospital, Denmark, PMID 10532689; 1 case from Department of Vascular Medicine, Academic Medical Center at the University of Amsterdam, The Netherlands, PMID 11810272; 1 case from Robarts Research Institute, Canada, PMID 11668627; 1 case submitted to ClinVar from U4M - Lille University & CHRU Lille, France. One proband with LDLC >10mmol/l and xanthoma, reported by Jiang et al, 2016, Department of atherosclerosis, Capital Medical University, China, PMID 27830735.
Met criteria codes
PS1
One other missense variant that leads to the same amino acid change at same codon, NM_000527.5 (LDLR):c.2475C>A (p.Asn825Lys), (ClinVarID 252341), is classified as Pathogenic by these guidelines.
PP4
Variant meets PM2 and is identified in >1 index cases who fulfil FH diagnostic criteria after alternative causes of high cholesterol were excluded.
PP3
REVEL = 0.803
PM2
PopMax MAF = 0.00002 in European (Non-Finnish) in gnomAD (gnomAD v2.1.1).
PS4_Supporting
Variant meets PM2 and is identified in 5 index cases who fulfil FH diagnostic criteria. Four index cases met DLCN criteria for definite or probable FH: 1 case from Department of Medicine and Cardiology, Aarhus Amtssygehus University Hospital, Denmark, PMID 10532689; 1 case from Department of Vascular Medicine, Academic Medical Center at the University of Amsterdam, The Netherlands, PMID 11810272; 1 case from Robarts Research Institute, Canada, PMID 11668627; 1 case submitted to ClinVar from U4M - Lille University & CHRU Lille, France. One proband with LDLC >10mmol/l and xanthoma, reported by Jiang et al, 2016, Department of atherosclerosis, Capital Medical University, China, PMID 27830735.
Not Met criteria codes
PS3
Functional data is not available.
Approved on: 2023-03-20
Published on: 2023-03-31
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